pySTDLM.PostProcessing Namespace Reference

Functions
def	openLMFile
	Open a Lattice Microbes File for reading. More...
def	closeLMFile
	Close a Lattice Microbes File. More...
def	showTraceFromFile
	Show species trace from a particular replicate. More...
def	plotTraceFromFile
	Plot species from an output file. More...
def	showTrace
	Show a specific species trace. More...
def	plotTrace
	Plot a specific species trace. More...
def	showAvgVarFromFile
	Show species from an output file. More...
def	plotAvgVarFromFile
	Plot species from an output file. More...
def	showAvgVar
	Show a specific species average over time and variance. More...
def	plotAvgVar
	Plot a specific species average over time and variance. More...
def	getOccupancyKymograph
	Compute the specie density(occupancy) among a slice of the simulation domain as a function over time for the given direciton. More...
def	plotOccupancyKymograph
	Plot a specific specie density(occupancy) among a slice of the simulation domain as a function of a direction over time. More...
def	showOccupancyKymograph
	Show a specific specie density(occupancy) among a slice of the simulation domain as a function of a direction over time. More...
def	plotPhaseSpace
	Plot the 2D or 3D phase space associated with the given species over the replicates indicated. More...
def	getTimesteps
	Extract the timestep times. More...
def	getSpecieTrace
	Extract data for a particular specie for the specified replicate. More...
def	getAvgVarTrace
	Get the average and variance of the specie trace over time. More...
def	getHistogram
	Get the histogram for a specie. More...
def	getPhaseSpace
	Get the nD phase space associated with the traces of species. More...

Function Documentation

def pySTDLM.PostProcessing.closeLMFile

(

f

)

Close a Lattice Microbes File.

Parameters

f	A previously opened lattice microbes file

def pySTDLM.PostProcessing.getAvgVarTrace	(		f,
			specie,
			doublingTime = None
	)

Get the average and variance of the specie trace over time.

Parameters

f	The HDF5 file handle to extract from or the name of a file to open
specie	The specie to extract
doublingTime	An optional doubling time parameter that will normalize average each trace by time in the cell cycle assuming exponentially growing cell (2log2 * x/2^(t/DT)), effectively normalizing against cell size. Default: no averaging is performed

Returns

avg, var, time

def pySTDLM.PostProcessing.getHistogram	(		f,
			species
	)

Get the histogram for a specie.

Parameters

f	The HDF5 file handle to extract from or the name of a file to open
specie	An array of specie/s to extract. returns a nD histogram of the data.

Returns

bins, edges (len(bins)+1)

def pySTDLM.PostProcessing.getOccupancyKymograph	(		f,
			species = None,
			replicate = 1
	)

Compute the specie density(occupancy) among a slice of the simulation domain as a function over time for the given direciton.

Parameters

filename	Name of file to extract data from
specie	A particular specie to plot density for
replicate	The replicate to show trace for

def pySTDLM.PostProcessing.getPhaseSpace	(		f,
			species,
			replicate
	)

Get the nD phase space associated with the traces of species.

If a single replicate is specified, a single trace will be returned, otherwise a 2/3D density matrix will be returned.

Parameters

f	The HDF5 file handle to extract from or the name of a file to open
specie	An iterable of 2 more specie names
replicate	The replicate for which to extract the phase space

Returns

A numpy array of a trace from a single replicate (specie1, specie2, ...)

def pySTDLM.PostProcessing.getSpecieTrace	(		f,
			specie,
			replicate = 1,
			doublingTime = None
	)

Extract data for a particular specie for the specified replicate.

Parameters

f	The HDF5 file handle to extract from or the name of a file to open
specie	The specie to extract data
replicate	The number of the replicate to extract from (default: 1)
doublingTime	An optional doubling time parameter that will normalize average each trace by time in the cell cycle assuming exponentially growing cell (2log2 * x/2^(t/DT)), effectively normalizing against cell size. Default: no averaging is performed

Returns

The species time trace in a numpy array

def pySTDLM.PostProcessing.getTimesteps

(

f

)

Extract the timestep times.

Parameters

f	The HDF5 file handle to extract from or the name of a file to open

Returns

The timestep times in a numpy array

def pySTDLM.PostProcessing.openLMFile

(

filename

)

Open a Lattice Microbes File for reading.

Parameters

filename

Name of the file

Returns

a handle to the file

def pySTDLM.PostProcessing.plotAvgVar	(		f,
			species = None,
			filename = None,
			kwargs
	)

Plot a specific species average over time and variance.

Parameters

f	An h5py object handle
species	A list of species to show
filename	A filename to print to (default None, gives the same behavior as showAvgVar(...))
kwargs	Additional arguments to be passed on to matplotlib.plot. These are any arguments that are valid with matplotlib.plot

Returns

A handle to the figure object created which allows customization of plot attributes

def pySTDLM.PostProcessing.plotAvgVarFromFile	(		filename,
			species,
			outfile,
			kwargs
	)

Plot species from an output file.

Parameters

filename	The name of an HDF5 output file generated by LatticeMicrobes
species	A list of species to plot
kwargs	Additional arguments to be passed on to matplotlib.plot. These are any arguments that are valid with matplotlib.plot
outfile	A filename to plot to

def pySTDLM.PostProcessing.plotOccupancyKymograph	(		f,
			species = None,
			replicate = 1,
			filename = None
	)

Plot a specific specie density(occupancy) among a slice of the simulation domain as a function of a direction over time.

Parameters

f	The name of the LM file
specie	A particular specie to plot density for
filename	A filename to print to (default None, gives the same behavior as showAvgVar(...))
replicate	The replicate to show trace for

def pySTDLM.PostProcessing.plotPhaseSpace	(		f,
			species = None,
			replicate = 1,
			withHistogram = False
	)

Plot the 2D or 3D phase space associated with the given species over the replicates indicated.

Parameters

f	An h5py object handle
specie	An iterable of 2 or 3 specie names indicating whether to plot in 2D or 3D space
replicate	The replicate to show trace for
withHistogram	If set to true, a heatmap of the phase space over all replicates will be plotted in the background. (NOTE: this only works in 2D.)

def pySTDLM.PostProcessing.plotTrace	(		f,
			species = None,
			replicate = 1,
			filename = None,
			kwargs
	)

Plot a specific species trace.

Parameters

f	An h5py object handle
species	A specie name or a list of species to show; can be a single string or a iterable list of species
filename	A filename to print to (default None, gives the same behavior as showAvgVar(...))
replicate	The replicate to show trace for. Can be an integer or an iterable list of replicte numbers
kwargs	Additional arguments to be passed on to matplotlib.plot. These are any arguments that are valid with matplotlib.plot

Returns

A handle to the figure object created which allows customization of plot attributes

def pySTDLM.PostProcessing.plotTraceFromFile	(		filename,
			species,
			replicate,
			outfile,
			kwargs
	)

Plot species from an output file.

Parameters

filename	The patch to an HDF5 output file generated by LatticeMicrobes
species	A list of species to plot
replicate	The replicate to show trace for
kwargs	Additional arguments to be passed on to matplotlib.plot. These are any arguments that are valid with matplotlib.plot
outfile	A filename to plot to

def pySTDLM.PostProcessing.showAvgVar	(		f,
			species,
			kwargs
	)

Show a specific species average over time and variance.

Parameters

f	An h5py object handle
species	A list of species to show
kwargs	Additional arguments to be passed on to matplotlib.plot. These are any arguments that are valid with matplotlib.plot

def pySTDLM.PostProcessing.showAvgVarFromFile	(		filename,
			species,
			kwargs
	)

Show species from an output file.

Parameters

filename	The name of an HDF5 output file generated by LatticeMicrobes
species	A list of species to plot
kwargs	Additional arguments to be passed on to matplotlib.plot. These are any arguments that are valid with matplotlib.plot

def pySTDLM.PostProcessing.showOccupancyKymograph	(		f,
			species = None,
			replicate = 1
	)

Show a specific specie density(occupancy) among a slice of the simulation domain as a function of a direction over time.

Parameters

f	An h5py object handle
specie	A particular specie to plot density for
replicate	The replicate to show trace for

def pySTDLM.PostProcessing.showTrace	(		f,
			species,
			replicate,
			kwargs
	)

Show a specific species trace.

Parameters

f	An h5py object handle
species	A list of species to show
replicate	The replicate to show trace for
kwargs	Additional arguments to be passed on to matplotlib.plot. These are any arguments that are valid with matplotlib.plot

def pySTDLM.PostProcessing.showTraceFromFile	(		filename,
			species,
			replicate,
			kwargs
	)

Show species trace from a particular replicate.

Parameters

filename	The patch to an HDF5 output file generated by LatticeMicrobes
species	A list of species to plot
replicate	The replicate to show trace for
kwargs	Additional arguments to be passed on to matplotlib.plot. These are any arguments that are valid with matplotlib.plot